Cystinuria: an inborn cause of urolithiasis

Effect of urine alkalization on urinary inflammatory markers in cystinuric patients

Background

Cystinuria is associated with a high prevalence of chronic kidney disease (CKD). We previously described a urinary inflammatory-protein signature (UIS), including 38 upregulated proteins, in cystinuric patients (Cys-patients), compared with healthy controls (HC). This UIS was higher in Cys-patients with CKD. In the present observational study, we aimed to investigate the UIS in Cys-patients without CKD and patients with calcium nephrolithiasis (Lith-patients), versus HC and the effect of urine alkalization on the UIS of Cys-patients.

Methods

UIS was evaluated by nano-liquid chromatography coupled to high-resolution mass spectrometry in adult HC, Lith-patients and non-treated Cys-patients with an estimated glomerular filtration rate >60 mL/min/1.73 m2, and after a 3-month conventional alkalizing treatment in Cys-patients.

Results

Twenty-one Cys-patients [12 men, median age (interquartile range) 30.0 (25.0-44.0) years], 12 Lith-patients [8 men, 46.2 (39.5-54.2) years] and 7 HC [2 men, 43.1 (31.0-53.9) years] were included. Among the 38 proteins upregulated in our previous work, 11 proteins were also upregulated in Cys-patients compared with HC in this study (5 circulating inflammatory proteins and 6 neutrophil-derived proteins). This UIS was also found in some Lith-patients. Using this UIS, we identified two subclusters of Cys-patients (5 with a very high/high UIS and 16 with a moderate/low UIS). In the Cys-patients with very high/high UIS, urine alkalization induced a significant decrease in urinary neutrophil-derived proteins.

Conclusion

A high UIS is present in some Cys-patients without CKD and decreases under alkalizing treatment. This UIS could be a prognostic marker to predict the evolution towards CKD in cystinuria.

Molecular identification of missense variants in SLC3A1 gene; an approach leading to computer-aided drug design for cystinuria

Cystinuria is a rare congenital disorder characterized by the formation of cystine stones in urinary system, mainly kidneys and urinary tract. It follows the autosomal recessive inheritance pattern, where both of the parents contain the mutant allele. Cystine is an oxidized dimeric form of amino acid cysteine, shining crystal of greenish-yellow color sized greater than 5 mm. A minor genetic defect in SLC3A1 gene, downregulate the cystine transporter, rBAT protein, to absorb cystine and other dibasic amino acids in proximal tubule of nephron, causing Cystinuria. Computational and molecular analysis of SLC3A1 gene was performed to identify the deleterious missense single nucleotide variations (mSNVs) linked with Cystinuria in Pakistani population. In silico analysis of whole SLC3A1 gene nsSNPs has revealed that the exon 1, 6 and 10 are the hotspot areas, which potentially alter the protein structure and function. Three SNVs including one synonymous SNV A186C in exon 1, and two mSNVs including G314T in exon 1 and G44972A in exons 10 were identified. Both mSNVs were confirmed by ARMS PCR in all the 68 samples. The results have shown that 10% of the patients have G314T, 16% have G44972A and 74% of the patients have both of these mSNVs. Both of these mSNVs were involved in the structural and functional deterioration of rBAT protein. Additionally, computer aided drug designing tools were used to design diaminobenzylpyrimidine drug around the mutant residues which exhibit the lowest binding affinity with the target as compared to the previously reported cystine binding thiol drugs. In future, the present study could be extended to a large scale for mass screening of reported SNVs and mSNVs which, ultimately, lead to the development of knockouts for the functional studies and treatments.

Novel compound heterozygous pathogenic variants in the SLC3A1 gene in a Chinese family with cystinuria

BACKGROUND

Cystinuria is an autosomal recessive disorder characterized by a cystine transport deficiency in the renal tubules due to mutations in two genes: SLC3A1 and SLC7A9. Cystinuria can be classified into three forms based on the genotype: type A, due to mutations in the SLC3A1 gene; type B, due to mutations in the SLC7A9 gene; and type AB, due to mutations in both genes.

METHODS

We report a 12-year-old boy from central China with cystine stones. He was from a non-consanguineous family that had no known history of genetic disease. A physical examination showed normal development and neurological behaviors. Whole-exome and Sanger sequencing were used to identify and verify the suspected pathogenic variants.

RESULTS

The compound heterozygous variants c.898_905del (p.Arg301AlafsTer6) is located in exon5 and c.1898_1899insAT (p.Asp634LeufsTer46) is located in exon10 of SLC3A1 (NM_000341.4) were deemed responsible for type A cystinuria family. The variant c.898_905del was reported in a Japanese patient in 2000, and the variant c.1898_1899insAT is novel.

CONCLUSION

A novel pathogenic heterozygous variant pair of the SLC3A1 gene was identified in a Chinese boy with type A cystinuria, enriching the mutational spectrum of the SLC3A1 gene. We attempted to find a pattern for the association between the genotype of SLC3A1 variants and the manifestations of cystinuria in patients with different onset ages. Our findings have important implications for genetic counseling and the early clinical diagnosis of cystinuria.

Gene purging and the evolution of Neoave metabolism and longevity

Maintenance of the proteasome requires oxidative phosphorylation (ATP) and mitigation of oxidative damage, in an increasingly dysfunctional relationship with aging. SLC3A2 plays a role on both sides of this dichotomy as an adaptor to SLC7A5, a transporter of branched-chain amino acids (BCAA: Leu, Ile, Val), and to SLC7A11, a cystine importer supplying cysteine to the synthesis of the antioxidant glutathione. Endurance in mammalian muscle depends in part on oxidation of BCAA; however, elevated serum levels are associated with insulin resistance and shortened lifespans. Intriguingly, the evolution of modern birds (Neoaves) has entailed the purging of genes including SLC3A2, SLC7A5, -7, -8, -10, and SLC1A4, -5, largely removing BCAA exchangers and their interacting Na+/Gln symporters in pursuit of improved energetics. Additional gene purging included mitochondrial BCAA aminotransferase (BCAT2), pointing to reduced oxidation of BCAA and increased hepatic conversion to triglycerides and glucose. Fat deposits are anhydrous and highly reduced, maximizing the fuel/weight ratio for prolonged flight, but fat accumulation in muscle cells of aging humans contributes to inflammation and senescence. Duplications of the bidirectional α-ketoacid transporters SLC16A3, SLC16A7, the cystine transporters SLC7A9, SLC7A11, and N-glycan branching enzymes MGAT4B, MGAT4C in Neoaves suggests a shift to the transport of deaminated essential amino acid, and stronger mitigation of oxidative stress supported by the galectin lattice. We suggest that Alfred Lotka's theory of natural selection as a maximum power organizer (PNAS 8:151,1922) made an unusually large contribution to Neoave evolution. Further molecular analysis of Neoaves may reveal novel rewiring with applications for human health and longevity.

Identification of mutations in 15 nephrolithiasis-related genes leading to a molecular diagnosis in 85 Chinese pediatric patients

BACKGROUND

The aim of this study was to describe the genotypic and phenotypic characteristics of Chinese pediatric patients with hereditary nephrolithiasis.

METHODS

Whole-exome sequencing (WES) was performed on 218 Chinese pediatric patients with kidney stones, and genetic and clinical data were collected and analyzed retrospectively.

RESULTS

The median age at onset in our cohort was 2.5 years (age range, 0.3-13 years). We detected 79 causative mutations in 15 genes, leading to a molecular diagnosis in 38.99% (85/218) of all cases. Monogenic mutations were present in 80 cases, and digenic mutations were present in 5 cases; 34.18% (27/79) of mutations were not included in the databases. Six common mutant genes, i.e., HOGA1, AGXT, GRHPR, SLC3A1, SLC7A9, and SLC4A1, were found in 84.71% of the patients overall. Furthermore, three mutations (A278A, c.834_834 + 1GG > TT, and C257G) in HOGA1, two mutations (K12QfX156 and S275RfX28) in AGXT, and one mutation (C289DfX22) in GRHPR represented hotspot mutations. The patients with HOGA1 mutations had the earliest onset age (0.8 years), followed by those with SLC7A9 (1.8 years), SLC4A1 (2.7 years), AGXT (4.3 years), SLC3A1 (4.8 years), and GRHPR (8 years) mutations (p = 0.002). Nephrocalcinosis was most commonly observed in patients with AGXT gene mutations.

CONCLUSIONS

Fifteen causative genes were detected in 85 Chinese pediatric patients with kidney stone diseases. The most common mutant genes, novel mutations, hotspot mutations, and genotype-phenotype correlations were also found. This study contributes to the understanding of genetic profiles and clinical courses in pediatric patients with hereditary nephrolithiasis. A higher resolution version of the Graphical abstract is available as Supplementary information.

Clinical Course and Mutational Analysis of Patients with Cystine Stone: A Single-Center Experience

Cystinuria is a known genetic disorder. To date, two genes, SLC3A1 and SLC7A9, have been identified as causes of cystinuria. In this study of 10 patients with cystinuria, which is the largest Korean cohort ever studied, we examined the patients' phenotypes, clinical courses, and genetic analyses. A total of 10 patients with cystinuria diagnosed with cystine stones in a single tertiary medical center (Severance Hospital, Seoul, Republic of Korea) from April 2000 to July 2023 were included in the study. All of the patients participated in mutational studies, and the clinical presentation and consecutive laboratory findings of the patients were analyzed retrospectively. After the initial stone-related surgery or procedure at our hospital, 6 of the 10 patients underwent additional surgery at least once for recurrent stones. Genetic analyses identified six new mutations, of which only two patients had type B mutations. The most common genotype was compound heterozygous type A. We investigated the genotypes and clinical courses of 10 Korean patients with cystinuria who had not been previously reported. More data are needed to statistically analyze the genotype and phenotype of cystinuria.

Interpretation of SLC3A1 and SLC7A9 variants in cystinuria patients: The significance of the PM3 criterion and protein stability

Cystinuria is a genetic disorder caused by defects in the b0,+ transporter system, which is composed of rBAT and b0,+AT coded by SLC3A1 and SLC7A9, respectively. Variants in SLC3A1 and SLC7A9 follow autosomal recessive inheritance and autosomal dominant inheritance with reduced penetrance, respectively, which complicates the interpretation of cystinuria-related variants. Here, we report seven different SLC3A1 variants and six different SLC7A9 variants. Among these variants were two novel variants previously not reported: SLC3A1 c.223C > T and SLC7A9 c.404A > G. In silico analysis using REVEL correlated well with the functional loss upon SLC7A9 variants with scores of 0.8560-0.9200 and 0.4970-0.5239 for severe and mild decrease in transport activity, respectively. In addition, DynaMut2 was able to predict a decreased protein expression level resulting from the SLC7A9 variant c.313G > A with a ΔΔGStability -2.93 kcal/mol. Our study adds to the literature as additional cases of a variant allow applying the PM3 criterion with higher strength level. In addition, we suggest the clinical utility of REVEL and DynaMut2 in interpreting SLC3A1 and SLC7A9 variants. While a decreased protein expression level is not embraced in the current variant interpretation guidelines, we believe in silico protein stability predicting tools could serve as evidence of protein function loss.

Cystine Stones: Developments in Minimally Invasive Surgery and Their Impact on Morbidity and Stone Clearance

Cystinuria is a rare genetic condition that is responsible for cystine stones. Besides stone recurrence, patients with cystine stones have reduced health-related quality of life, increased rates of chronic kidney disease and hypertension. Although lifestyle measures, medical therapy and close follow up are essential to reduce and monitor cystine stone recurrences, surgical intervention is frequently needed for most cystinuria patients. Shock wave lithotripsy, ureteroscopy, percutaneous nephrolithotomy and active surveillance all have a role, and technological advances in endourology are vital in achieving a stone-free status and to prevent recurrences. The complexity of managing cystine stones necessitates a multidisciplinary team discussion, patient involvement and an individualised approach in a specialist centre for optimum management. Thulium fibre laser and virtual reality may have an increasing role in the future of cystine stone management.

Use of whole-exome sequencing to identify novel monogenic gene mutations and genotype-phenotype correlations in Chinese Han children with urolithiasis

The incidence of urolithiasis (UL) in children has been increasing. Although the pathogenesis of pediatric UL is controversial and remains unclear, multiple monogenic causes of UL have been identified. We aim to investigate the prevalence of inherited UL causes and explore the genotype-phenotype correlation in a Chinese pediatric group. In this study, we analyzed the DNA of 82 pediatric UL patients using exome sequencing (ES). The data of metabolic evaluation and genomic sequencing were subsequently analyzed together. We detected 54 genetic mutations in 12 of 30 UL-related genes. A total of 15 detected variants were described as pathogenic mutations, and 12 mutations were considered likely pathogenic. Molecular diagnoses were made in 21 patients with pathogenic or likely pathogenic variants. Six novel mutations that were not previously reported were identified in this cohort. Calcium oxalate stones were detected in 88.9% cases (8/9) with hyperoxaluria-related mutations, while 80% of individuals (4/5) with cystinuria-causing defects were diagnosed with cystine stones. Our study highlights the significant genetic abnormalities in pediatric UL and demonstrates the diagnostic power of ES for screening patients with UL.

Genetic and clinical analysis of Chinese pediatric patients with cystinuria

This study aimed to investigate the genotypic and phenotypic characteristics of Chinese pediatric patients with cystinuria. This was a retrospective study of 14 Chinese pediatric patients with cystine stones. All published studies of the Chinese pediatric cystinuria population were searched and enrolled based on the inclusive standard. Among the 14 pediatric patients with cystinuria, 8 were males and 6 were females. The mean age of first stone onset was 4.0 ± 3.3 years (4 months-9 years). All of the patients had multiple stones, and 57.1% (8/14) had bilateral stones. The mean maximum stone diameter was 1.7 ± 0.6 (range 0.5-2.6) cm. A total of 13 SLC3A1 gene mutations and 9 SLC7A9 gene mutations were detected, of which 41% (9/22) of mutations were novel. Patients with SLC7A9 mutations were more likely to develop bilateral stones than those with SLC3A1 mutations (100% vs. 33.3%, p = 0.03). Thirty-four SLC3A1 gene mutations and twenty-eight SLC7A9 gene mutations were found in a total of fifty-five Chinese children with cystinuria. The SLC7A9 gene mutation distribution was more dispersed, while the SLC3A1 mutation was clustered in exons 6-8. The c.647C > T (p. T216M) (4/53) and c.1113C > A (p. Y371Ter) (4/53) mutations in the SLC3A1 gene and the c.1399 + 2_3insT (3/36) mutation in the SLC7A9 gene represent potential hotspots in cystinuria. Our results present a comprehensive genetic spectrum for pediatric cystinuria patients in China. Patients with SLC7A9 mutations were more likely to develop bilateral stones than those with SLC3A1 mutations. A wide mutation spectrum and the potential mutation hotspots associated with cystinuria were also identified.

Cystinuria: an update on pathophysiology, genetics, and clinical management

Cystinuria is the most common genetic cause of nephrolithiasis in children. It is considered a heritable aminoaciduria as the genetic defect affects the reabsorption of cystine and three other amino acids (ornithine, lysine, and arginine) in the renal proximal tubule. Patients affected by this condition have elevated excretion of cystine in the urine, and because of this amino acid's low solubility at normal urine pH, patients tend to form cystine calculi. To date, two genes have been identified as disease-causative: SLC3A1 and SLC7A9, encoding for the two subunits of the heterodimeric transporter. The clinical features of this condition are solely related to nephrolithiasis. The diagnosis is usually made during infancy or adolescence, but cases of late diagnosis are common. The goal of therapy is to reduce excretion and increase the solubility of cystine, through both modifications of dietary habits and pharmacological treatment. However, therapeutic interventions are not always sufficient, and patients often have to undergo several surgical procedures during their lives to treat recurrent nephrolithiasis. The goal of this literature review is to synthesize the available evidence on diagnosis and management of patients affected by cystinuria in order to provide physicians with a practical tool that can be used in daily clinical practice. This review also aims to shed some light on new therapy directions with the aim of ameliorating kidney outcomes while improving adherence to treatment and quality of life of cystinuric patients.

Novel "Turn-On" Luminescent Chemosensor for Arginine by Using a Lanthanide Metal-Organic Framework Photosensitizer

Arginine is considered as a biomarker of cystinuria and other diseases, and thus, it is of urgency to develop a simple and rapid method with high sensitivity and selectivity for arginine detection to meet the demand of on-site analysis and bedside diagnosis. In this work, a lanthanide metal-organic framework, La(TATB), was prepared using a triazine-based planar ligand, 4,4',4″-s-triazine-2,4,6-triyltribenzoate (H₃TATB), and lanthanide ion (La³⁺). La(TATB) can be used as a highly photosensitive agent to activate molecular oxygen to ¹O₂ to achieve efficient photosensitive oxidation of arginine accompanied by strong blue fluorescence emission under 302 nm UV irradiation. Due to the porous structure and high specific surface area of La(TATB), short-life ¹O₂ can effectively approach and react with amino acid substrate molecules, thus leading to higher sensitivity than other systems. Therefore, the "turn-on" fluorescence sensing of trace arginine can be realized, with a measured linear response range of 10-20,000 nM and a limit of detection as low as 7 nM. This method can be used for the detection of trace arginine in urine, which is conducive to the bedside diagnosis and rapid screening of cystinuria and other diseases. The proposed method not only expands the application scope of Ln-MOFs but also provides a new construction strategy for "turn-on" luminescence sensors.

Gene therapy for kidney disease: targeting cystinuria

PURPOSE OF REVIEW

The aim of this study was to summarize recent findings in kidney gene therapy while proposing cystinuria as a model kidney disease target for genome engineering therapeutics.

RECENT FINDINGS

Despite the advances of gene therapy for treating diseases of other organs, the kidney lags behind. Kidney-targeted gene delivery remains an obstacle to gene therapy of kidney disease. Nanoparticle and adeno-associated viral vector technologies offer emerging hope for kidney gene therapy. Cystinuria represents a model potential target for kidney gene therapy due to its known genetic and molecular basis, targetability, and capacity for phenotypic rescue.

SUMMARY

Although gene therapy for kidney disease remains a major challenge, new and evolving technologies may actualize treatment for cystinuria and other kidney diseases.

Coexistence of Megaconial Congenital Muscular Dystrophy and Cystinuria: Mimicking Hypotonia-Cystinuria Syndrome

<b><i>Introduction:</i></b> Hypotonia-cystinuria syndrome is a contiguous gene deletion syndrome that is characterized by hypotonia, developmental delay, and cystinuria type A. We present a male patient who was admitted to our center with clinical findings of hypotonia-cystinuria syndrome and diagnosed with megaconial congenital muscular dystrophy and cystinuria. <b><i>Case Presentation:</i></b> A 16-month-old male patient was admitted with complaints of restlessness and body laxity. It was stated that the patient had hypotonia and growth retardation at the age of 2 months. Physical examination revealed mild hypotonia, growth retardation, and development delay, while laboratory examinations identified elevated serum creatine kinase and elevated dibasic amino acid in urine analysis. Because of the findings of hypotonia, growth retardation, developmental delay, and cystinuria, hypotonia-cystinuria syndrome was considered as a differential diagnosis. However, by chromosomal microarray no contiguous deletion in region 2p21 was found, while a novel homozygous c.225-2A&#x3e;T pathogenic variant in the <i>CHKB</i> gene and a c.1266_1267delGT heterozygous variant in the <i>SLC7A9</i> gene inherited from the mother were identified with whole-exome sequencing. The co-occurrence of megaconial congenital muscular dystrophy and cystinuria, mimicking hypotonia-cystinuria syndrome, was confirmed. <b><i>Conclusion:</i></b> This case suggests that in countries with a high frequency of consanguineous marriage, even if the molecular genetic analysis results are not compatible with the clinical findings, it should be kept in mind that different genetic diseases may coexist.

Composition of urinary stones in children: clinical and metabolic determinants in a French tertiary care center

As the epidemiology of urolithiasis is constantly evolving, analyzing the composition of stones is crucial to better understand the determinants of lithogenesis. The aim of this study was to describe the composition of stones of pediatric patients in a tertiary center. Clinical and metabolic data from all pediatric patients with at least one stone that was analyzed by Fourier transformed infrared spectroscopy (FTIR) in the Hospices Civils de Lyon between 2013 and 2017 were retrospectively collected. A total of 111 patients (sex ratio 1.4:1) were included; their median ([IQR]) age was 7.5 (3.1-10.5) years. The main component of stones was calcium oxalate (weddellite for 34 (31%) stones, whewellite 23 (21%)), calcium phosphate (carbapatite 32 (29%), brushite 6 (5%), amorphous calcium phosphate 3 (3%)), struvite 5 (5%), cystine 4 (4%), uric acid 2 (2%), and ammonium acid urate 2 (2%). A total of 20 (18%) stones were pure and 24 (22%) were infectious. Carbapatite stones were the most frequent in patients < 2 years and calcium oxalate stones in patients > 2 years old. Metabolic abnormalities (most frequently hypercalciuria) were found in 50% of tested patients and in 54% of patients with infectious stones. Congenital anomalies of the kidney and/or urinary tract (CAKUT) or neurogenic bladder were present in 9/24 (38%) patients with infectious stones and 12/16 (76%) patients with bladder stones.Conclusion: This study confirms that calcium oxalate stones are the most frequent among pediatric patients, which could reflect the nutritional habits of predisposed patients. In contrast, infectious stones are less frequent and occur mostly in association with anatomic or metabolic favoring factors.

A case of early onset cystinuria in a 4-month-old girl

Cystinuria is an autosomal recessive disorder characterized by a decrease in the reabsorption of cystine and dibasic amino acids (lysine, ornithine, and arginine) in the renal proximal tubule. It presents with recurrent urolithiasis. Cystinuria accounts for 6-8% of all pediatric urolithiasis. The age of onset is typically 10-30 years. Here, we report a case of early-onset cystinuria. A 4-month-old girl presented with hematuria. We noticed multiple renal calculi in ultrasonography and abdominal computerized tomography scans. The diagnosis was cystinuria with urinary calculus analysis and urinary amino acid analysis. The patient was treated with urine alkalinization and cystine chelating drugs. Gene analysis showed a P482L heterozygous mutation from her mother, and an A70V heterozygous mutation from her father, in the SLC7A9 gene. This gene encodes a putative subunit of the neutral and basic amino acid transport protein, BAT1. Although cystinuria is an autosomal recessive disease, there have been previous reports of P482L heterozygous mutations greatly suppressing cystine reabsorption and causing cystinuria symptoms. Therefore, the highly influential P482L mutation of the SLC7A9 gene may have contributed to the onset of this autosomal recessive disease at an extremely young age.

Safety profile of D-penicillamine: a comprehensive pharmacovigilance analysis by FDA adverse event reporting system

BACKGROUND

D-penicillamine (D-pen) is a copper-chelating drug and has immune-modulatory properties. D-pen is used to treat rheumatoid arthritis, Wilson's disease, and kidney stones (cystinuria). However, associated adverse events (AEs) of D-pen treatment are frequent and often serious. Therefore, a comprehensive assessment of the safety profile of D-pen is urgently needed.

RESEARCH DESIGN AND METHODS

We identified and analyzed AEs associated with D-pen between April-1970 to July-2020 from the U.S. Food and Drug Administration Adverse Event Reporting System (FAERS) databases and calculated the reported odds ratio (ROR) with 95% confidence intervals (CI) using the disproportionality analysis.

RESULTS

A total of 9,150,234 AEs related to drugs were reported in the FAERS database, of which 542 were related to D-Pen. We report that D-pen was associated with dystonia (ROR: 20.52; 95%CI: 12.46-33.80), drug hypersensitivity (ROR: 5.42; 95%CI: 3.72-7.90), pancytopenia (ROR: 10.20; 95%CI: 5.61-18.56), joint swelling (ROR: 9.07; 95%CI: 5.51-14.94), renal-impairment (ROR: 6.68; 95%CI: 3.67-12.15), dysphagia (ROR: 5.05; 95%CI: 2.76-8.89), aggravation of condition (ROR: 4.16; 95%CI: 2.60-6.67), congestive cardiac failure (ROR: 4.04; 95%CI: 2.22-7.35), peripheral edema (ROR: 3.77; 95%CI: 2.17-6.55), tremor (ROR: 3.46; 95%CI: 2.00-6.01), pyrexia (ROR: 3.46; 95%CI: 2.00-6.01), and gait disturbance (ROR: 2.41; 95%CI: 1.29-4.52).

CONCLUSIONS

Patients taking D-pen require close monitoring of renal function, blood counts, immunity, liver, cardiac function, and neurological function. D-pen suppresses immune system which maximizes the risk of infection.

[Cystinuria]

Cystinuria is the most common monogenic nephrolithiasis disorder. Because of its poor solubility at a typical urine pH of less than 7, cystine excretion results in recurrent urinary cystine stone formation. A high prevalence of high blood pressure and of chronic kidney disease has been reported in these patients. Alkaline hyperdiuresis remains the cornerstone of the preventive medical treatment. To reach a urine pH between 7.5 and 8 and a urine specific gravity less than or equal to 1.005 should be the goal of medical treatment. D-penicillamine and tiopronin, two cysteine-binding thiol agents, should be considered as second line treatments with frequent adverse events that should be closely monitored.

The Impact of Diet on Urinary Risk Factors for Cystine Stone Formation

Despite the importance of dietary management of cystinuria, data on the contribution of diet to urinary risk factors for cystine stone formation are limited. Studies on the physiological effects of diet on urinary cystine and cysteine excretion are lacking. Accordingly, 10 healthy men received three standardized diets for a period of five days each and collected daily 24 h urine. The Western-type diet (WD; 95 g/day protein) corresponded to usual dietary habits, whereas the mixed diet (MD; 65 g/day protein) and lacto-ovo-vegetarian diet (VD; 65 g/day protein) were calculated according to dietary reference intakes. With intake of the VD, urinary cystine and cysteine excretion decreased by 22 and 15%, respectively, compared to the WD, although the differences were not statistically significant. Urine pH was significantly highest on the VD. Regression analysis showed that urinary phosphate was significantly associated with cystine excretion, while urinary sulfate was a predictor of cysteine excretion. Neither urinary cystine nor cysteine excretion was affected by dietary sodium intake. A lacto-ovo-vegetarian diet is particularly suitable for the dietary treatment of cystinuria, since the additional alkali load may reduce the amount of required alkalizing agents.

Hyperechoic Content of the Fetal Colon Is Not Always Cystinuria-Case Report

Cystinuria is a recessively inherited genetic disease causing recurrent kidney stones with risk of kidney failure. The discovery of hyperechoic colonic content on an antenatal ultrasound is considered to be a pathognomic sign of cystinuria. Herein, we present a clinical case with antenatal diagnosis of cystinuria in an ultrasound finding, which eventually revealed a multisystem disease, characterized by the association of renal Fanconi syndrome, hyperinsulinemic hypoglycemia, and hepatic dysfunction. Genetic investigations evidenced the recurrent heterozygous missense HNF4A (p.Arg76Trp) variant. Our case report shows that antenatal hyperechoic colonic content can hide a complex proximal renal tubulopathy, and questions the genetic counseling provided to families in the antenatal period.

Structural basis for amino acid exchange by a human heteromeric amino acid transporter

Heteromeric amino acid transporters (HATs) comprise a group of membrane proteins that belong to the solute carrier (SLC) superfamily. They are formed by two different protein components: a light chain subunit from an SLC7 family member and a heavy chain subunit from the SLC3 family. The light chain constitutes the transport subunit whereas the heavy chain mediates trafficking to the plasma membrane and maturation of the functional complex. Mutation, malfunction, and dysregulation of HATs are associated with a wide range of pathologies or represent the direct cause of inherited and acquired disorders. Here we report the cryogenic electron microscopy structure of the neutral and basic amino acid transport complex (b^[0,+]AT1-rBAT) which reveals a heterotetrameric protein assembly composed of two heavy and light chain subunits, respectively. The previously uncharacterized interaction between two HAT units is mediated via dimerization of the heavy chain subunits and does not include participation of the light chain subunits. The b^(0,+)AT1 transporter adopts a LeuT fold and is captured in an inward-facing conformation. We identify an amino-acid-binding pocket that is formed by transmembrane helices 1, 6, and 10 and conserved among SLC7 transporters.

Computational analysis identifies druggable mutations in human rBAT mediated Cystinuria

Culex quinquefasciatus Cqm1 protein acts as the receptor for Lysinibacillus sphaericus mosquito-larvicidal binary (BinAB) toxin that is used worldwide for mosquito control. We found amino acid transporter protein, rBAT, as phylogenetically closest Cqm1 homolog in humans. The present study reveals large evolutionary distance between Cqm1 and rBAT, and rBAT ectodomain lacks the sequence motif which serves as binding-site for the BinAB toxin. Thus, BinAB toxin can be expected to remain safe for humans. rBAT (heavy subunit; SLC3A1) and catalytic b^0,+AT (light subunit; SLC7A9), linked by single disulfide bond, mediate renal reabsorption of cystine and dibasic amino acids in Na⁺ independent manner. Mutations in rBAT cause type I Cystinuria disease which shows global prevalence, and rBAT can be thought as an important pharmacological target. However, 3D structures of rBAT and b^0,+AT, the two components of b^0,+ heteromeric amino acid transporter systems, are not available. We constructed a reliable homology model of rBAT using Cqm1 coordinates and that of transmembrane b^0,+AT subunit using LAT1 coordinates. Mapping of pathogenic mutations onto rBAT ectodomain revealed their scattered distribution throughout the rBAT protein. Further, our computational simulations-based scoring of several known deleterious mutations of rBAT revealed that mutations those do not compromise the protein fold and stability, are localized on the same face of the molecule. These residues are expected to interact with the b^0,+AT transporter. The present study thus identifies druggable sites on rBAT that could be targeted for the treatment of type I Cystinuria.Communicated by Ramaswamy H. Sarma.

Update on cystine stones: current and future concepts in treatment

Cystine stones are relatively uncommon compared with other stone compositions, constituting just 1% to 2% of adult urinary tract stone diseases, and accounting for up to 10% of pediatric stone diseases. Two responsible genes of cystinuria have been identified, the SLC3A1 and the SLC7A9. Cystinuria is diagnosed by family history, stone analysis, or by measurement of urine cystine excretion. Current treatments for cystinuria include increased fluid intake to increase cystine solubility by maintaining daily urine volume of greater than 3 Liter (L). Limiting sodium and protein intake can decrease cystine excretion. When conservative therapy fails, then pharmacologic therapy may be effective. Alkaline urine pH in the 7.0-7.5 range will reduce cystine solubility and can be achieved by the addition of alkali therapy. If these measures fail, cystine-binding thiol drugs such as tiopronin and D-penicillamine are considered. These compounds bind cysteine and prevent the formation of less soluble cystine. These drugs, however, have poor patient compliance due to adverse effects. Captopril can be useful in the treatment of cystine stones but the drug has not been tested in rigorous clinical trials. Novel potential therapies such as alpha-lipoic acid and crystal growth inhibitors (L-cystine dimethyl ester (L-CDME) and L-cystine methyl ester (L-CME)) were developed and tested in animals. Those therapies showed promising results. Compliance with treatment was associated with a lower rate of cystine stone formation.

Genetic and Clinical Analyses of 13 Chinese Families With Cystine Urolithiasis and Identification of 15 Novel Pathogenic Variants in SLC3A1 and SLC7A9

Background

Cystinuria is a rare genetic disorder characterized by defective renal reabsorption of cystine, ornithine, arginine, and lysine. The increased urinary excretion of cystine results in the development of cystine urolithiasis (CU). The mutated SLC3A1 and SLC7A9 genes are the cause of CU, a global disorder. Its frequency and mutation spectrum vary between different populations. In Asia, the data for CU are limited.

Method

Urinary stones were collected from patients of a single center over a five-year period and analyzed via Fourier transform infrared spectroscopy. Genomic DNA was isolated from 13 patients with CU and their parents and from 26 controls affected by calcium oxalate dihydrate stones. The coding regions and the exon-intron boundaries of SLC3A1 and SLC7A9 were subjected to PCR amplification and then sequenced via traditional Sanger sequencing. Genetic variants were functionally annotated using the InterVar, ClinVar, gnom AD, and HGMD databases.

Results

From the 232 samples of urinary stones, we identified 13 patients with CU (10 males and 3 females). The onset age was from 7 months to 9 years. The CU stones varied from 0.26 cm³ to 18.67 cm³. Sanger sequencing detected a total of 14 SLC3A1 (nine were novel) and 10 SLC7A9 (six were novel) rare variants from the 13 CU families. All variants, including 15 novel variants, were pathogenic, disease-causing, or damaging.

Conclusion

All 13 pediatric CU families harbored SLC3A1 or/and SLC7A9 rare variants. A total of 15 novel pathogenic variants in SLC3A1 and SLC7A9 were identified. This study expanded the known mutational spectrum of CU in the Chinese population.

Educational review: role of the pediatric nephrologists in the work-up and management of kidney stones

BACKGROUND

The incidence of nephrolithiasis in children and adolescents is increasing and appears to double every 10 years. The most important role of the pediatric nephrologist is to diagnose and modify various metabolic and non-metabolic risk factors, as well as prevent long-term complications especially in the case of recurrent nephrolithiasis.

OBJECTIVE

The purpose of this review is to summarize the existing literature on the etiology and management of pediatric nephrolithiasis.

RESULTS

The incidence of kidney stones is increasing; dietary and environmental factors are probably the main causes for this increased incidence. In most pediatric patients, the etiology for the kidney stones can be identified. Metabolic factors, such as hypercalciuria and hypocitraturia, urinary tract infection, and urinary stasis, constitute leading causes. Herein, we review the etiologies, diagnostic work-up, and treatment options for the most prevalent causes of kidney stones. The detrimental effects of excessive dietary sodium, reduced fluid intake, and the benefits of plant-based over animal-based protein consumption on urinary crystal formation are discussed. We also review the long-term complications.

CONCLUSIONS

Pediatric nephrologists have an important role in the diagnostic work-up and prevention of recurring nephrolithiasis.

The effect of additional drug therapy as metaphylaxis in patients with cystinuria: a systematic review

INTRODUCTION

To systematically review the effect of additional drug therapy as metaphylaxis in patients with cystinuria.

EVIDENCE ACQUISITION

A literature search of three databases (MEDLINE, Embase and the Cochrane Library) was performed according to the PRISMA-guidelines enclosing articles published up to May 2019. A total of 1117 articles were screened. Thirty-four publications met the inclusion criteria for this review.

EVIDENCE SYNTHESIS

Male-female ratio in the studied cohorts was 49.9% - 50.1%. The majority of studies showed a positive effect in reducing stone events and/or urinary cystine excretion. D-Penicillamine showed success in 13/14 (92%) studies, whereas Tiopronin-treatment showed a reduction in all (8/8; 100%) studies. All studies on Captopril (4/4) showed a decrease, however not all significant. The same is true for studies on Thiols in combination with Captopril (2/2). Furthermore, Tiopronin showed less side effects compared to D-penicillamine, respectively 30% and 37%. Captopril showed the least adverse events, with one event in nine patients.

CONCLUSIONS

The evidence on benefit of additional drug therapy in patients with cystinuria is scarce. All studied medications showed an effect on stone event and urinary cystine excretion, when used in addition to hyperhydration, alkalization and a diet low on methionine. Based on this systematic review, no drug can be preferred over another. An important aspect in the choice of drug is the risk of side effects. Therefore, the choice of additional drug should be personalized for every patient where the risk of side effects should be taken into consideration.

CRISPR/Cas9 engineering of albino cystinuria Type A mice

Cystinuria Type A is a relatively common genetic kidney disease occurring in 1 in 7,000 people worldwide that results from mutation of the cystine transporter rBAT encoded by Slc3a1. We used CRISPR/Cas9 technology to engineer cystinuria Type A mice via genome editing of the C57BL/6NHsd background. These mice are an improvement on currently available models as they are on a coisogenic genetic background and have a single defined mutation. In order to use albinism to track Cas9 activity, we co-injected gRNAs targeting Slc3a1 and tyrosinase (Tyr) with Cas9 expressing plasmid DNA into mouse embryos. Two different Slc3a1 mutational alleles were derived, with homozygous mice of both demonstrating elevated urinary cystine levels, cystine crystals, and bladder stones. We used whole genome sequencing to evaluate for potential off-target editing. No off-target indels were observed for the top 10 predicted off-targets for Slc3a1 or Tyr. Therefore, we used CRISPR/Cas9 to generate coisogenic albino cystinuria Type A mice that could be used for in vivo imaging, further study, or developing new treatments of cystinuria.

Diversity of Phenotype and Genetic Etiology of 23 Cystinuria Saudi Patients: A Retrospective Study

Background: Cystinuria is an inborn error of metabolism that manifests with renal stones due to defective renal epithelial cell transport of cystine which resulted from pathogenic variants in the SLC3A1 and/or SLC7A9 genes. Among nephrolithiasis diseases, cystinuria is potentially treatable, and further stone formation may be preventable. We report 23 patients who were identified biochemically and genetically to have cystinuria showing the diversity of the phenotype of cystinuria and expanding the genotype by identifying a broad spectrum of mutations. Patients and Methods: This is a multicenter retrospective chart review, where clinical and biochemical data, genetic analysis and the progress of the disease were documented over five years at two centers from 2014 to 2019. Results: Of 23 patients who were identified biochemically and/or genetically to have cystinuria, 14 (62%) were male. Thirteen patients were homozygous, and two were heterozygous for the SLC3A1 gene. Seven were homozygous and one was compound heterozygous for the SLC7A9 gene. We have detected 12 genetic variants including five novel variants. SLC3A1 gene variant c.1400 T > A (p.Met467Lys) is found in 38% of our cohort. Although 21 patients required surgical intervention, none developed ESRD. The number of stone episodes per year varied widely (median frequency of 0.45 stones/ per year, range between 0.06 and 78.2), with no significant difference in stone events per year between sexes (P = 0.73). Conclusion: Despite the high rate of consanguinity in Saudi Arabia, there was a broad spectrum of genetic variants. Most of our patients are homozygous recessive for SLC genes with multiple generations affected which indicates early screening and prevention of disease in these families. Phenotypic heterogeneity is well documented in our cohort even with the same genotype and the first stone episode age was variable but most commonly seen in the first decade of life.

Amino Acid Transport Defects in Human Inherited Metabolic Disorders

Amino acid transporters play very important roles in nutrient uptake, neurotransmitter recycling, protein synthesis, gene expression, cell redox balance, cell signaling, and regulation of cell volume. With regard to transporters that are closely connected to metabolism, amino acid transporter-associated diseases are linked to metabolic disorders, particularly when they involve different organs, cell types, or cell compartments. To date, 65 different human solute carrier (SLC) families and more than 400 transporter genes have been identified, including 11 that are known to include amino acid transporters. This review intends to summarize and update all the conditions in which a strong association has been found between an amino acid transporter and an inherited metabolic disorder. Many of these inherited disorders have been identified in recent years. In this work, the physiological functions of amino acid transporters will be described by the inherited diseases that arise from transporter impairment. The pathogenesis, clinical phenotype, laboratory findings, diagnosis, genetics, and treatment of these disorders are also briefly described. Appropriate clinical and diagnostic characterization of the underlying molecular defect may give patients the opportunity to avail themselves of appropriate therapeutic options in the future.

The genetic landscape of the human solute carrier (SLC) transporter superfamily

The human solute carrier (SLC) superfamily of transporters is comprised of over 400 membrane-bound proteins, and plays essential roles in a multitude of physiological and pharmacological processes. In addition, perturbation of SLC transporter function underlies numerous human diseases, which renders SLC transporters attractive drug targets. Common genetic polymorphisms in SLC genes have been associated with inter-individual differences in drug efficacy and toxicity. However, despite their tremendous clinical relevance, epidemiological data of these variants are mostly derived from heterogeneous cohorts of small sample size and the genetic SLC landscape beyond these common variants has not been comprehensively assessed. In this study, we analyzed Next-Generation Sequencing data from 141,456 individuals from seven major human populations to evaluate genetic variability, its functional consequences, and ethnogeographic patterns across the entire SLC superfamily of transporters. Importantly, of the 204,287 exonic single-nucleotide variants (SNVs) which we identified, 99.8% were present in less than 1% of analyzed alleles. Comprehensive computational analyses using 13 partially orthogonal algorithms that predict the functional impact of genetic variations based on sequence information, evolutionary conservation, structural considerations, and functional genomics data revealed that each individual genome harbors 29.7 variants with putative functional effects, of which rare variants account for 18%. Inter-ethnic variability was found to be extensive, and 83% of deleterious SLC variants were only identified in a single population. Interestingly, population-specific carrier frequencies of loss-of-function variants in SLC genes associated with recessive Mendelian disease recapitulated the ethnogeographic variation of the corresponding disorders, including cystinuria in Jewish individuals, type II citrullinemia in East Asians, and lysinuric protein intolerance in Finns, thus providing a powerful resource for clinical geneticists to inform about population-specific prevalence and allelic composition of Mendelian SLC diseases. In summary, we present the most comprehensive data set of SLC variability published to date, which can provide insights into inter-individual differences in SLC transporter function and guide the optimization of population-specific genotyping strategies in the bourgeoning fields of personalized medicine and precision public health.

A highly selective and sensitive fluorescent sensor based on Tb3+-functionalized MOFs to determine arginine in urine: a potential application for the diagnosis of cystinuria

A unique metal-organic framework with the formula [Cd₄(H₂L)₂(L)·H₂O]·3H₂O (H₄L = 5,5'-(1H-1,2,4-triazole-3,5-diyl)diisophthalic acid) was successfully constructed under solvothermal conditions. The frameworks with multiple free Lewis base sites and Lewis acid sites exhibited easily sensitized properties. After the encapsulation of Tb³⁺ cations, the as-synthesized Tb³⁺@Cd-MOF demonstrated strong luminescence induced by the efficient energy transfer from the bridging ligands to the Tb³⁺ cations, with the potential to serve as a chemical sensor. Interestingly, Tb³⁺@Cd-MOF was proven to be a very promising and highly selective and sensitive luminescent platform for the quantitative detection of arginine, which is the biomarker of cystinuria. The fluorescent probe presented high selectivity to arginine in urine with strong luminescence quenching. Furthermore, a convenient fluorescence-based test paper for the visual detection of arginine in applications was prepared. For the first time, arginine was quantified and monitored in urine by a highly efficient recyclable fluorescent sensor based on Tb³⁺-functionalized MOF hybrids, which may be a potential candidate for the further development of clinical diagnostic tools.

Metabolic consequences of cystinuria

Background

Cystinuria is an inherited disorder of renal amino acid transport that causes recurrent nephrolithiasis and significant morbidity in humans. It has an incidence of 1 in 7000 worldwide making it one of the most common genetic disorders in man. We phenotypically characterized a mouse model of cystinuria type A resultant from knockout of Slc3a1.

Methods

Knockout of Slc3a1 at RNA and protein levels was evaluated using real-time quantitative PCR and immunofluorescence. Slc3a1 knockout mice were placed on normal or breeder chow diets and evaluated for cystine stone formation over time suing x-ray analysis, and the development of kidney injury by measuring injury biomarkers. Kidney injury was also evaluated via histologic analysis. Amino acid levels were measured in the blood of mice using high performance liquid chromatography. Liver glutathione levels were measured using a luminescent-based assay.

Results

We confirmed knockout of Slc3a1 at the RNA level, while Slc7a9 RNA representing the co-transporter was preserved. As expected, we observed bladder stone formation in Slc3a1^−/− mice. Male Slc3a1^−/− mice exhibited lower weights compared to Slc3a1^+/+. Slc3a1^−/− mice on a regular diet demonstrated elevated blood urea nitrogen (BUN) without elevation of serum creatinine. However, placing the knockout animals on a breeder chow diet, containing a higher cystine concentration, resulted in the development of elevation of both BUN and creatinine indicative of more severe chronic kidney disease. Histological examination revealed that these dietary effects resulted in worsened kidney tubular obstruction and interstitial inflammation as well as worsened bladder inflammation. Cystine is a precursor for the antioxidant molecule glutathione, so we evaluated glutathione levels in the livers of Slc3a1^−/− mice. We found significantly lowered levels of both reduced and total glutathione in the knockout animals.

Conclusions

Our results suggest that that diet can affect the development and progression of chronic kidney disease in an animal model of cystinuria, which may have important implications for patients with this disease. Additionally, reduced glutathione may predispose those with cystinuria to injury caused by oxidative stress.

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Electronic supplementary material

The online version of this article (10.1186/s12882-019-1417-8) contains supplementary material, which is available to authorized users.

Outcomes and Long-term Follow-up of Patients with Cystine Stones: a Systematic Review

PURPOSE OF REVIEW

Cystine stone patients can be difficult to manage with frequent recurrences. We performed a systematic review with a view to assessing interventions, compliance and their long-term outcomes.

RECENT FINDINGS

Ten retrospective observational studies (253 patients) assessed the outcomes and long-term follow-up of cystine stone patients. The mean length of follow-up was 9.6 years (range 3.5-21.8 years). The overall mean number of surgical procedures/patient was 5.7 (range 2-9.8/patient) with the overall mean number of surgical procedures/patient/year at 0.59 (range 0.22-1.32/patient/year). While open surgery has decreased over the last decade and PCNL has been stable, there seems to be a rise of RIRS during this period. Patients with cystine stones need periodic interventions for stone recurrences despite medical management, with limited data showing the impact on renal function. While the management is individualised, wide variability exists with often poor and incomplete patient data.

Polymorphism in the PBX1 gene is related to cystinuria in Brazilian families

The aim of our study was to determine regions of loss of heterozygosity, copy number variation analysis, and single nucleotide polymorphisms (SNPs) in Brazilian patients with cystinuria. A linkage study was performed using DNA samples from six patients with cystinuria and six healthy individuals. Genotyping was done with the Genome-Wide Human SNP 6.0 arrays (Affymetrix, Inc., Santa Clara, CA, USA). For validation, SNPs were genotyped using a TaqMan® SNP Genotyping Assay Kit. The homozygote polymorphic genotype of SNP rs17383719 in the gene PBX1 was more frequent (P = 0.015) in cystinuric patients. The presence of the polymorphic allele for this SNP increased the chance of cystinuria by 3.0-fold (P = 0.036). Pre-B-cell leukaemia transcription factor 1 (PBX1) was overexpressed 3.3-fold in patients with cystinuria. However, when we compared the gene expression findings with the genotyping, patients with a polymorphic homozygote genotype had underexpression of PBX1, while patients with a heterozygote or wild-type homozygote genotype had overexpression of PBX1. There is a 3-fold increase in the risk of the development of cystinuria among individuals with this particular SNP in the PBX1 gene. We postulate that the presence of this SNP alters the expression of PBX1, thus affecting the renal absorption of cystine and other amino acids, predisposing to nephrolithiasis.

A Case of Hypotonia-Cystinuria Syndrome With Genito-Urinary Malformations and Extrarenal Involvement

Hypotonia-Cystinuria syndrome (HCS) is a rare disease, caused by a mutation in two contiguous genes (SLC3A1 and PREPL) localized on chromosome 2p21, and it is characterized by both renal involvement with cystine stones and nervous involvement with hypotonia. We here describe a 2 years old child with HCS associated with other clinical features as congenital anomalies of kidney and urinary tract (primary obstructed megaureter, POM), cryptorchidism and cardiac involvement (patent foramen ovale with atrial septum aneurysm). To the best of our knowledge, cryporchidism and POM have never been reported before in patients with HCS. Moreover, a cardiac involvement has been described only in another case of HCS that, interestingly, presents the same genetic abnormalities as our patient. The diagnosis of HCS can be difficult because neurological signs are aspecific and kidney stones are commonly absent during the first months of life. A better understanding of the complete clinical scenario associated with HCS can help clinicians suspect, diagnose and treat HCS earlier with a positive influence on both neurological and renal outcome.

Cystinuria: genetic aspects, mouse models, and a new approach to therapy

Cystinuria, a genetic disorder of cystine transport, is characterized by excessive excretion of cystine in the urine and recurrent cystine stones in the kidneys and, to a lesser extent, in the bladder. Males generally are more severely affected than females. The disorder may lead to chronic kidney disease in many patients. The cystine transporter (b^0,+) is a heterodimer consisting of the rBAT (encoded by SLC3A1) and b^0,+AT (encoded by SLC7A9) subunits joined by a disulfide bridge. The molecular basis of cystinuria is known in great detail, and this information is now being used to define genotype-phenotype correlations. Current treatments for cystinuria include increased fluid intake to increase cystine solubility and the administration of thiol drugs for more severe cases. These drugs, however, have poor patient compliance due to adverse effects. Thus, there is a need to reduce or eliminate the risks associated with therapy for cystinuria. Four mouse models for cystinuria have been described and these models provide a resource for evaluating the safety and efficacy of new therapies for cystinuria. We are evaluating a new approach for the treatment of cystine stones based on the inhibition of cystine crystal growth by cystine analogs. Our ongoing studies indicate that cystine diamides are effective in preventing cystine stone formation in the Slc3a1 knockout mouse model for cystinuria. In addition to crystal growth, crystal aggregation is required for stone formation. Male and female mice with cystinuria have comparable levels of crystalluria, but very few female mice form stones. The identification of factors that inhibit cystine crystal aggregation in female mice may provide insight into the gender difference in disease severity in patients with cystinuria.

Prevalence of kidney stones in the USA: The National Health and Nutrition Evaluation Survey

Objective:

The National Health and Nutrition Examination Survey (NHANES) has demonstrated an upward trend in prevalence of kidney stones (KSs) in the past 30 years. We aim to report the current prevalence of KSs.

Methods:

Research was based upon a cross-sectional analysis of response to the 2007–2014 NHANES. The prevalence of self-reported KS history was calculated using weights and design factors reported by NHANES. Four cycles of NHANES data were analyzed separately (2007–2014), and KS-prevalence trends in adult individuals for different age groups were compared. Analysis was performed using SAS ver.9.4.

Results:

The prevalence of KSs was 10.1% for the last 2013–2014 NHANES cycle. The highest prevalence of KSs was observed in males older than 60 years, at 17.8%, followed by males 40–59 years old at 12.6%. This trend changes in the 20–39-year-old age group, wherein females had a higher prevalence than males—7.5% for females compared to 4.5% in males. Females in the study showed a steady increase in KSs prevalence through the study cycles: 6.6% in 2007 to 9.5% in 2013 ( p < 0.05). The increase in females ages 20 to 39, almost doubled in prevalence: 3.9 to 7.5%, from 2007 to 2013 ( p < 0.05). Females older than 60 years of age have remained stable, with prevalence of 8.9% in 2007 to 9.8% in 2013. Males showed a slight decrease in prevalence from 2007 to 2014, from 12.7% in 2007 to 11.4% in 2014. Prevalence in males and females older than 60 years old were relatively stable.

Conclusions:

Prevalence of KSs has remained stable in males and has increased in females. Females of child-bearing age showed the most significant increase. For this specific group, there has been a steady increase in the last seven years.

Level of evidence:

IV

No evidence for point mutations in the novel renal cystine transporter AGT1/SLC7A13 contributing to the etiology of cystinuria

BACKGROUND

Cystinuria is caused by the defective renal reabsorption of cystine and dibasic amino acids, and results in cystine stone formation. So far, mutations in two genes have been identified as causative. The SLC3A1/rBAT gene encodes the heavy subunit of the heterodimeric rBAT-b0,+AT transporter, whereas the light chain is encoded by the SLC7A9/ b0,+AT gene. In nearly 85% of patients mutations in both genes are detectable, but a significant number of patients currently remains without a molecular diagnosis. Thus, the existence of a further cystinuria gene had been suggested, and the recently identified AGT1/SLC7A13 represents the long-postulated partner of rBAT and third cystinuria candidate gene.

METHODS

We screened a cohort of 17 cystinuria patients for SLC7A13 variants which were negative for SLC3A1 and SLC7A9 mutations.

RESULTS

Despite strong evidences for an involvement of SLC7A13 mutations in cystinuria, we could not confirm a relevant role of SLC7A13 for the disease.

CONCLUSION

With the exclusion of SLC7A13/AGT1 as the third cystinuria gene accounting for the SLC3A1 and SLC7A9 mutation negative cases, it becomes obvious that other genetic factors should be responsible for the cystinuria phenotype in nearly 15% of patients.

Journey of a cystinuric patient with a long-term follow-up from a medical stone clinic: necessity to be SaFER (stone and fragments entirely removed)

There is a lack of studies looking at the longitudinal follow-up of patients with cystine stones. We wanted to assess the journey of cystinuric patients through our specialist metabolic stone clinic to improve the understanding of episodes, interventions and current outcomes in this patient cohort. After ethical approval, all patients who attended our metabolic stone clinic from 1994 to 2014 with at least one cystine stone episode were included in our study. Data were retrospectively analysed for patient demographics, stone episodes or intervention, clinical parameters and patient compliance. Over a period of 21 years, 16 patients with a median age of 15.5 years underwent a mean follow-up of 8.6 years (1–21 years). The mean number of surgical interventions was 3.1 (1–8/patient), but patients who were stone free after their first treatment had lower recurrences (p = 0.91) and lower number of interventions during their follow-up (2.7/patient, compared to those who were not stone free at 4/patient). During their follow-up period, patients with < 3 interventions had a significantly better renal function than those with ≥ 3 surgical interventions (p = 0.04). Additionally, linear regression analysis showed that eGFR was demonstrated to decline with increasing numbers of stone episodes (r² = 0.169). It was also noted that patients who began early medical management remained stone free during follow-up compared to those who had medical management after ≥ 2 stone episodes, of whom all had a recurrent episode. Our long-term longitudinal study of cystine stone formers highlights that patients who are stone free and receive early metabolic stone screening and medical management after their initial presentation have the lowest recurrence rates and tend to preserve their renal function. Hence, prompt referral for metabolic assessment, and the stone and fragments entirely removed (SaFER) principles are key to preventing stone episodes and improving long-term function.

Spectrum of mutations in cystinuria patients presenting with prenatal hyperechoic colon

Cystinuria is a heterogeneous, rare but important cause of inherited kidney stone disease due to mutations in 2 genes: SLC3A1 and SLC7A9. Antenatal hyperechoic colon (HEC) has been reported in some patients as a non-pathological consequence of the intestinal transport defect. We report 83 patients affected by cystinuria: 44 presented prenatally with a HEC (HEC group) and 39 with a classical postnatal form (CC group). SLC3A1 and SLC7A9 were sequenced. All patients were fully genotyped, and the relationship between the genotype and clinical features was analyzed. We identified mutations in SLC3A1 in 80% of the HEC group and in only 49% of the CC group. The SLC3A1 p.Thr216Met mutation was found in 21% of the alleles in the HEC group but was never found in the CC group. Most of the mutations found in the HEC group were considered severe mutations in contrast with the CC group. Twenty-five novel mutations were reported. This study shows a relationship between genotype and the clinical form of cystinuria, suggesting that only the patients with the most severe mutations presented with an HEC. These results emphasized the need for prenatal cystinuria screening using classical third-trimester ultrasound scan and the early management of suspected newborns.

Associating mutations causing cystinuria with disease severity with the aim of providing precision medicine

Background

Cystinuria is an inherited disease that results in the formation of cystine stones in the kidney, which can have serious health complications. Two genes (SLC7A9 and SLC3A1) that form an amino acid transporter are known to be responsible for the disease. Variants that cause the disease disrupt amino acid transport across the cell membrane, leading to the build-up of relatively insoluble cystine, resulting in formation of stones. Assessing the effects of each mutation is critical in order to provide tailored treatment options for patients. We used various computational methods to assess the effects of cystinuria associated mutations, utilising information on protein function, evolutionary conservation and natural population variation of the two genes. We also analysed the ability of some methods to predict the phenotypes of individuals with cystinuria, based on their genotypes, and compared this to clinical data.

Results

Using a literature search, we collated a set of 94 SLC3A1 and 58 SLC7A9 point mutations known to be associated with cystinuria. There are differences in sequence location, evolutionary conservation, allele frequency, and predicted effect on protein function between these mutations and other genetic variants of the same genes that occur in a large population. Structural analysis considered how these mutations might lead to cystinuria. For SLC7A9, many mutations swap hydrophobic amino acids for charged amino acids or vice versa, while others affect known functional sites. For SLC3A1, functional information is currently insufficient to make confident predictions but mutations often result in the loss of hydrogen bonds and largely appear to affect protein stability. Finally, we showed that computational predictions of mutation severity were significantly correlated with the disease phenotypes of patients from a clinical study, despite different methods disagreeing for some of their predictions.

Conclusions

The results of this study are promising and highlight the areas of research which must now be pursued to better understand how mutations in SLC3A1 and SLC7A9 cause cystinuria. The application of our approach to a larger data set is essential, but we have shown that computational methods could play an important role in designing more effective personalised treatment options for patients with cystinuria.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3913-1) contains supplementary material, which is available to authorized users.

[Rare metabolic disorders and urolithiasis]

Numerous metabolic anomalies, which often have no direct pathological relevance when considered individually, are found in all people. In most patients with urinary tract stones, it can be assumed that a specific combination or interaction of these anomalies occurs, thus, resulting in stone formation, but only after individual exogenous risk factors are triggered. Lithogenesis is the result of a cascade of different "events" that are temporally close to one another, but sometimes these events interact strong enough that significant stone growth occurs. Chronic metabolic disorders usually lead to permanently altered urine compositions. The occurrence of physiological urine constituents in nonnormal concentration ratios and/or the nonphysiological excretion of metabolic products can significantly increase the lithogenicity of urine, so that urolithiasis can manifest itself as a clinical symptom. In cases of urolithiasis of unknown origin, a potentially hidden rare metabolic anomaly should always be considered. In addition, if a patient has a known metabolic disease, then this should always be taken into account as a risk factor for stone formation and attempts should be taken to clarify its influence on urine composition. This also applies to the efficacy of a therapy. A distinct link between a metabolic disease and stone formation is generally rare and will likely remain so despite significant advances regarding differential diagnosis and etiopathology. This article focuses on very rare metabolic causes and/or genetic syndromes which may be associated with urolithiasis. Patients receiving symptomatic stone treatment should receive life-long follow-up care from a urologist because reducing the recurrence rate helps to improve the quality of life of the patients.

Report of SLC3A1/rBAT gene mutations in Iranian cystinuria patients: A direct sequencing study

Background:

Considering a few studies on the genetic basis of the cystinuria in the Middle East and the population-specific distribution of mutations in the SLC3A1, we tried to find genetic variants in three exons (1, 3, and 8) of SLC3A1.

Materials and Methods:

In this study, exons 1, 3, and 8 of SLC3A1 gene of 25 unrelated cystinuria patients searched for genetic variations by polymerase chain reaction and sequencing.

Results:

There were five different variations in our studied population. We found one mutation in the SLC3A1 gene including missense variant M467K and identified three polymorphisms: nonsynonymous variant G38G, c. 610 + 169C>T and c. 610 + 147C>G within the SLC3A1 gene, and one new variant.

Conclusion:

Our results confirm that cystinuria is a heterogeneous disorder at the molecular level and more studies are needed to identify the distribution and frequency of mutations causing cystinuria in the Iranian population.

Delineation of cystinuria in Saudi Arabia: A case series

BACKGROUND

Cystinuria is an inherited metabolic disease that is caused by defects in two genes, SLC3A1 and SLC7A9, which result in a renal reabsorptive defect of cystine and other dibasic amino acids, including ornithine, arginine, and lysine. Patients usually present with recurrent renal calculi and may develop renal impairment. Medical management includes high fluid intake and chelating agents. To the best of our knowledge, this is the first study describing cystinuria in Saudi Arabia.

METHODS

A retrospective chart review for cystinuria patients from the genetic and nephrology divisions between 2010 to 2015. All patients were investigated, diagnosed and treated at King Abdulaziz Medical City in Saudi Arabia.

RESULTS

Eight patients were identified from five unrelated families. The age of onset ranged from birth to 14 years. The female to male ratio was 1.7:1. Two new variants in the SLC3A1 and SLC9A7 genes were discovered. All of the detected mutations were missense variants in three different exons, such as c.1711 T > A (p.Cys571Ser) (exon 10), c.1166C > T p.Thr389Met (exon 11) and c.1400 T > A p.Met467Lys (exon 8). Additionally, 37.5% of our patients developed arterial hypertension and 25% had urinary tract infection, but none had renal impairment. No significant clinical differences were detected in this study between type A (SLC3A1 variants) and type B cystinuria (SLC7A9 variant). Two cases were diagnosed based on clinical information, biochemical testing and a positive family history as all of the molecular testing for cystinuria was negative.

CONCLUSION

Cystinuria has wide genetic heterogeneity with a poor genotype/phenotype correlation. Negative molecular investigations should not rule out the disease if clinical and biochemical investigations support the diagnosis. A larger data registry is essential to better describe the cystinuria genotype/phenotype in Saudi Arabia.

Genotype and Phenotype Analysis in Pediatric Patients with Cystinuria

Cystinuria is an inherited disorder characterized by defective renal reabsorption of cystine and dibasic amino acids leading to nephrolithiasis. This study was conducted to analyze the genotypes and phenotypes of pediatric patients with cystinuria. Eight children from Seoul National University Hospital and Asan Medical Center presenting with cystinuria from January 2003 to June 2016 were retrospectively analyzed. Mutational studies were performed by direct sequencing. Two of the 8 were male and 6 were female. The median ages at onset and diagnosis were 1.5 (range, 0.3-13.6) and 2.6 (range, 0.7-16.7) years, respectively. The median followed up was 7.7 (range, 3.4-14.0) years. Mutational analyses were performed in 7 patients and revealed biallelic SLC3A1 mutations (AA genotype) in 4 patients, a single heterozygous SLC3A1 mutation (A- genotype) in 1 patient, biallelic SLC7A9 mutations (BB genotype) in 1 patient, and a single heterozygous SLC7A9 mutation (B- genotype) in 1 patient. Two of the mutations were novel. No genotype-phenotype correlations were observed, except for earlier onset age in patients with non-AA genotypes than in patients with the AA genotype. All patients suffered from recurrent attacks of symptomatic nephrolithiasis, which lead to urologic interventions. At the last follow-up, 3 patients had a mild-to-moderate degree of renal dysfunction. This is the first study of genotypic and phenotypic analyses of patients with cystinuria in Korea.

Case Report: Cystinuria and Polycystic Kidney Disease

Cystinuria and polycystic kidney disease are 2 genetic disorders that affect the genitourinary tract but rarely together. This case report presents 2 pediatric patients diagnosed with polycystic kidney disease and cystinuria requiring surgical treatment. Both subjects presented acutely with stone disease. Imaging studies and stone analysis established the diagnoses. Although coexistence of these 2 conditions is rare, cystinuria should be considered in the differential diagnosis when evaluating patients with cystic disease who develop renal calculi.

Genetic defects underlying renal stone disease

Renal stones are common and are usually secondary to risk factors affecting the solubility of substances in the urinary tract. Primary, that is genetic, causes are rare but nevertheless are important to recognise so that appropriate treatments can be instigated and the risks to other family members acknowledged. A brief overview of the investigation of renal stones from a biochemical point of view is presented with emphasis on the problems that can arise. The genetic basis of renal stone disease caused by (i) derangement of a metabolic pathway, (ii) diversion to an insoluble product, (iii) failure of transport and (iv) renal tubular acidosis is described by reference to the disorders of adenine phosphoribosyl transferase (APRT) deficiency, primary hyperoxaluria, cystinuria and autosomal dominant distal renal tubular acidosis.

Cystinuria Associated with Different SLC7A9 Gene Variants in the Cat

Cystinuria is a classical inborn error of metabolism characterized by a selective proximal renal tubular defect affecting cystine, ornithine, lysine, and arginine (COLA) reabsorption, which can lead to uroliths and urinary obstruction. In humans, dogs and mice, cystinuria is caused by variants in one of two genes, SLC3A1 and SLC7A9, which encode the rBAT and bo,+AT subunits of the bo,+ basic amino acid transporter system, respectively. In this study, exons and flanking regions of the SLC3A1 and SLC7A9 genes were sequenced from genomic DNA of cats (Felis catus) with COLAuria and cystine calculi. Relative to the Felis catus-6.2 reference genome sequence, DNA sequences from these affected cats revealed 3 unique homozygous SLC7A9 missense variants: one in exon 5 (p.Asp236Asn) from a non-purpose-bred medium-haired cat, one in exon 7 (p.Val294Glu) in a Maine Coon and a Sphinx cat, and one in exon 10 (p.Thr392Met) from a non-purpose-bred long-haired cat. A genotyping assay subsequently identified another cystinuric domestic medium-haired cat that was homozygous for the variant originally identified in the purebred cats. These missense variants result in deleterious amino acid substitutions of highly conserved residues in the bo,+AT protein. A limited population survey supported that the variants found were likely causative. The remaining 2 sequenced domestic short-haired cats had a heterozygous variant at a splice donor site in intron 10 and a homozygous single nucleotide variant at a branchpoint in intron 11 of SLC7A9, respectively. This study identifies the first SLC7A9 variants causing feline cystinuria and reveals that, as in humans and dogs, this disease is genetically heterogeneous in cats.